**IMPORTANT!**
IgPhyML has moved to https://github.com/immcantation/igphyml

To update Git configuration settings use:

```
   git config user.email "your-gh-user@email.com"
   git config user.name "your-gh-user-name"
   git remote set-url origin git@github.com:immcantation/igphyml.git
```

IgPhyML - B cell phylogenetic inference package
================================================================================

IgPhyML is a program designed to build phylogenetic trees and test evolutionary
hypotheses regarding B cell affinity maturation.

The biology of B cell somatic hypermutation (SHM) violates important assumptions
in most standard phylogenetic substitution models; further, while most
phylogenetics programs are designed to analyze single lineages, B cell
repertoires typically contain thousands of lineages. IgPhyML addresses both of
these issues by implementing substitution models that correct for the
context-sensitive nature of SHM, and combines information from multiple lineages
to give more precisely estimated repertoire-wide model parameter estimates.

IgPhyML is integrated into the Immcantation framework, meaning users can easily
build and visualize B cell lineage trees and test hypotheses about mutation and
selection in B cell repertoires.